Electron energy loss measurements have been made on a series of fluorine labelled biological molecules which were coated onto thin carbon substrates. The fluorine K edge as well as the carbon, nitrogen and oxygen K edges were measured as a function of electron dose in order to establish the rate of mass loss of fluorine. This was sone by scanning the incident electron probe over a well defined area while recording the beam current using a Faraday cup. Some of the compounds investigated are closely related to neurotransmitters and it was established that these could withstand a dose of several thousand electrons per angstrom squared.